I was wondering if is wrong to use TPM for differential gene expression analysis from RNA sequence data. The samples that I want to compare is technically the same cell line but treated one is untreated and the other is treated with a drug. I have read that TMM should be used if you are comparing different samples or different tissue or different cell line. However, in my case even though I am comparing different samples the cell line is the same the difference is that one group is treated with a drug while the other is not.
The reason why I am asking the question is because the group bioinformatics (who doesn't really have a biology background) insists that we have to use TMM because we are comparing different samples. However, I think TPM is fine here because technically it is the same cell line but treated different. I know that TMM is used when comparing samples from different origins or different cell lines.
Lastly, looking at the data normalized via both methods, the TPM data make more sense and correlates with actual biological validations that I have done in the lab and the literature. Any input is greatly appreciated